Subdomain Mapping [moved]

I am a user of cPanel, and I have a question on how subdomains are currently set up.

Using the xcontroller theme, when I create a subdomain, it currently maps it to its respective folder in public_html/, allowing users to access it from http://sub.domain.com/ as well as http://www.domain.com/sub/.

I do not want the latter option to exist, so my question is, is it possible to change where subdomains are mapped to? I would prefer it to map them to a subdomains/ folder outside of the public_html/ folder.

There are many frustrating reasons for this request, so any help would be appreciated. Thanks!

That brings me to my next question. Where is httpd.conf located and how can I access it? I have root access to the server, I just can't seem to find a file manager or anything above domain level access in cpanel.